Protocols

IsoformSwitchAnalyzeR specifications

Information


Unique identifier OMICS_19008
Name IsoformSwitchAnalyzeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Maintainer


  • person_outline Kristoffer Vitting-Seerup

Publications for IsoformSwitchAnalyzeR

IsoformSwitchAnalyzeR citation

call_split

ICE1 promotes the link between splicing and nonsense mediated mRNA decay

2018
eLife
PMCID: 5896957
PMID: 29528287
DOI: 10.7554/eLife.33178.037
call_split See protocol

[…] lysis of differential gene and isoform usage with Kallisto/Sleuth (; ). To identify transcript isoforms violating the 50–55 nt rule, the longest ORF in each TACO-derived transcript was annotated with IsoformSwitchAnalyzeR (). The most highly expressed isoform from each gene, as judged by the transcripts per million (TPM) Kallisto calculation, was used to compute 3’UTR lengths for downstream gene-l […]

IsoformSwitchAnalyzeR institution(s)
The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
IsoformSwitchAnalyzeR funding source(s)
Supported by grants from the Lundbeck Foundation and the Independent Research Fund Denmark.

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